dartR: gl2sa – R documentation

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gl2sa

Convert genlight objects to the format used in the SNPassoc package

Description

This function exports a genlight object into a SNPassoc object. See package SNPassoc for details. #' This function needs package SNPassoc. At the time of writing (August 2020) the package was no longer available from CRAN. To install the package check their github repository. https://github.com/isglobal-brge/SNPassoc and/or use install_github("isglobal-brge/SNPassoc") to install the function and uncomment the function code.

Usage

gl2sa(x, verbose = NULL, installed = FALSE)

Arguments

`x`	– name of the genlight object containing the SNP data [required]
`verbose`	– verbosity: 0, silent or fatal errors; 1, begin and end; 2, progress log ; 3, progress and results summary; 5, full report [default 2 or as specified using gl.set.verbosity]
`installed`	switch to run the function once SNPassoc package is installed

Value

Returns an object of class 'snp' to be used with SNPassoc.

Author(s)

Bernd Guber (Post to https://groups.google.com/d/forum/dartr)

References

Gonzalez, J.R., Armengol, L., Sol?, X., Guin?, E., Mercader, J.M., Estivill, X. and Moreno, V. (2017). SNPassoc: an R package to perform whole genome association studies. Bioinformatics 23:654-655.

dartR

Importing and Analysing SNP and Silicodart Data Generated by Genome-Wide Restriction Fragment Analysis

v1.9.6

GPL-2

Authors

Bernd Gruber [aut, cre], Arthur Georges [aut], Jose L. Mijangos [aut], Peter J. Unmack [ctb], Oliver Berry [ctb], Lindsay V. Clark [ctb], Floriaan Devloo-Delva [ctb]

Initial release

2021-04-29